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From: InSuk Joung <i.joung.gmail.com>

Date: Thu, 29 Jul 2010 22:52:23 -0400

The alignment of the atoms are 1-2-3-4 and 2-3-4 are almost in a straight

line. I was aware that the dihedral angle is not defined actually. But,

the force constant was set zero so I wanted it to be zero rather than nan.

Sander definitely gives a finite dihedral energy.

In my specific case, uu = uv = 0.

On Thu, Jul 29, 2010 at 10:17 PM, case <case.biomaps.rutgers.edu> wrote:

*> On Thu, Jul 29, 2010, InSuk Joung wrote:
*

*> >
*

*> > Recently I posted a problem about the calculation of dihedral energy
*

*> using
*

*> > NAB to AMBER mailing list. I think I found the source of the problem
*

*> >
*

*> > At the 458th line of eff.c:
*

*> >
*

*> > uu = (aa * bb) - (ab * ab);
*

*> > vv = (bb * cc) - (bc * bc);
*

*> > uv = (ab * bc) - (ac * bb);
*

*> > den = 1.0 / sqrt(uu * vv);
*

*> > co = uv * den;
*

*> >
*

*> > When 'uu' or 'vv' is 0. 'den' goes to infinity, which causes a problem.
*

*> I
*

*> > am not sure if this way to calculate the dihedral angle is
*

*> computationally
*

*> > efficient but I believe dihedral angles can be calculated using atan2
*

*> > without the numerical problem. Can anybody suggest a detour for this?
*

*>
*

*> First, what is the geometry of the four atoms you are using here? Is
*

*> either
*

*> the 1-2-3 or the 2-3-4 angle 180 degrees? (Dihedral torsions are not well
*

*> defined in such cases).
*

*>
*

*> Second, when uu or vv are zero, is uv also zero?
*

*>
*

*> ....dac
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER-Developers mailing list
*

*> AMBER-Developers.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber-developers
*

*>
*

Date: Thu, 29 Jul 2010 22:52:23 -0400

The alignment of the atoms are 1-2-3-4 and 2-3-4 are almost in a straight

line. I was aware that the dihedral angle is not defined actually. But,

the force constant was set zero so I wanted it to be zero rather than nan.

Sander definitely gives a finite dihedral energy.

In my specific case, uu = uv = 0.

On Thu, Jul 29, 2010 at 10:17 PM, case <case.biomaps.rutgers.edu> wrote:

-- Best, InSuk Joung _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Thu Jul 29 2010 - 20:00:03 PDT

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